Viruses are one of the major groups of pathogens that attack plants, resulting in negative effects influencing relevant crop aspects such as plant growth, plant vigour, product quality, and yield potential. Like most eukaryotes, plants have established active defense mechanisms against invading pathogens, amongst which viruses.
Besides structural and physical barriers, like cell walls, that protect plants against pathogens, roughly three types of plant immune systems are currently recognized. The first type responds to molecules from many classes of microbes, using transmembrane pattern recognition receptors (PPRs) that can react to microbial associated molecular patterns (MAMPs) and pathogen-associated molecular patterns (PAMPs).
The second type of plant immune system uses the polymorphic NB-LRR (nucleotide binding leucine rich repeat) protein products encoded by resistance (R) genes. The NB-LRR proteins are able to detect pathogen effector proteins or their activity from diverse sources. On the pathogen side, a specific avirulence (Avr) protein or effector, encoded by Avr genes, triggers the R-protein-mediated immune responses by the host plant. The R gene and Avr action/reaction causes the hypersensitive response (HR), one of the most common plant reactions to many types of pathogenic organisms. However, despite the availability of several cloned R genes and their corresponding Avr proteins, it is still not fully clear how pathogen Avr proteins are recognized by their host.
A third important defense mechanism that plants use to defend themselves against viruses or other pathogens is based on RNA silencing or RNA interference. RNA silencing refers to a class of gene silencing effects by which the expression of one or more genes is downregulated or entirely suppressed by small RNAs. A number of gene families and their related protein families have been identified as components of the RNA silencing system. Amongst those are Dicer (DCR) genes, Dicer-Like (DCL) genes, Argonaute (AGO) nuclease genes, and RNA-dependent RNA polymerase (RDR) genes. Each of those gene families contains several members, which can act in different combinations in different species, and have their own particular functionality and type of interaction against specific pathogens or groups of pathogens.
Upon viral infection of the host plant an RNA virus establishes viral replication, resulting in the presence of virally derived dsRNA. This dsRNA triggers the plant's RNA silencing system by functioning as a substrate for a specific DCL protein, an endoribonuclease, which cleaves the dsRNA into short fragments of typical lengths ranging from about 20-25 basepairs. After further processing, single-stranded forms of these short virus-derived siRNA fragments are loaded unto an AGO protein, which is part of the RNA-induced silencing complex (RISC) of the host plant. In the RISC, the siRNA is used by the AGO proteins as a guiding template which ultimately results in the degradation of viral RNA through a series of recognition and cleavage processes.
RDR genes are thought to play a role in this immunity system by the enhanced production of virus-specific dsRNA substrates for DCL proteins through de novo synthesis. The resulting siRNA accumulation then presumably increases the efficiency by which the recognition of the viral RNA occurs, which can consequently be more actively silenced or degraded.
As a counter measure many viruses have developed a system to circumvent or inhibit RNA silencing pathways, by activation of RNA silencing suppressors (RSS). The presence of a particular RSS can contribute to inhibition of the plant's defense, which in turn re-enables viral genome replication and spread in the targeted host plant, thereby facilitating further infection.
The balance between the silencing and suppressing pathways of a certain plant and a particular virus plays a large role in determining whether a virus will succeed in establishing an infection, or if the plant will prove strong enough to be completely or sufficiently resistant to withstand the attack.
Although the involvement of the various mentioned genes in plant immunity systems as such has been recognized, much about the regulatory mechanisms, the relationships between those genes, and the ways in which the different proteins function remains elusive. Moreover, the contribution of the individual genes to viral silencing, while overcoming the antisilencing of the pathogen, has not been resolved. In addition, further research to unravel the structure of the relevant genes and the way their expression is regulated is still ongoing.
Consequently, it is unclear which gene that is involved in the RNA silencing pathway would be a preferred candidate to target for inducing resistance against pathogens, in particular against viruses, and in which way it should be modified to obtain the desired effect.
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